in SESraster() removed co_* from resulting raster

HemingNM · Oct 21, 2024 · de810ca · de810ca
1 parent e2eeff4
commit de810ca
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Showing 2 changed files with 13 additions and 15 deletions.
diff --git a/R/SESraster.R b/R/SESraster.R
@@ -187,9 +187,9 @@ SESraster <- function(x,
   rast.rand <- terra::rast(rast.rand) # transform a list into a SpatRaster
 
   ## vector to store results
-  resu <- stats::setNames(as.double(rep(NA, 8)),
+  resu <- stats::setNames(as.double(rep(NA, 6)),
                           c("Observed","Null_Mean", "Null_SD", "SES",
-                            "co_lower", "co_upper", "p_lower", "p_upper"))
+                            "p_lower", "p_upper"))
 
   ## SES for multiple layers
   ses <- terra::rast(lapply(seq_len(nrow(rcomb)),
@@ -205,14 +205,12 @@ SESraster <- function(x,
 
                                                   nm <- mean(x[-1], na.rm=TRUE) ### Randomized mean value
                                                   nsd <- stats::sd(x[-1], na.rm=TRUE) ### Randomized stdev value
-                                                  co_lower <- sum((x[1] < x[-1]), na.rm = T) #Count of times observed value was lower than random values
-                                                  co_upper <- sum((x[1] > x[-1]), na.rm = T) # Count of times observed value was higher than random values
-                                                  p_lower <- co_lower / aleats # Calculate p-value for lower tail
-                                                  p_upper <- co_upper / aleats # Calculate p-value for upper tail
+                                                  p_lower <- sum((x[1] < x[-1]), na.rm = T)/aleats # Count of times observed value was lower than random values and calculate p-value
+                                                  p_upper <- sum((x[1] > x[-1]), na.rm = T)/aleats # Count of times observed value was higher than random values and calculate p-value
 
                                                   resu[] <- c(x[1], nm, nsd,
                                                               ifelse(nsd==0, (x[1]-nm), (x[1]-nm)/nsd),
-                                                              co_lower, co_upper, p_lower, p_upper)
+                                                              p_lower, p_upper)
 
                                                   return(resu)
 
@@ -224,7 +222,7 @@ SESraster <- function(x,
 
                             }, ro = rast.obs, rr = rast.rand, rcomb = rcomb, resu = resu,
                             mi = mi,
-                            cores = cores, aleats, temp.filename = temp.filename,
+                            cores = cores, aleats = aleats, temp.filename = temp.filename,
                             overwrite = overwrite, ...))
 
   if(filename != ""){

diff --git a/tests/testthat/test-SESraster.R b/tests/testthat/test-SESraster.R
@@ -10,15 +10,15 @@ test_that("SES works", {
   # test ses by species
   ses <- SESraster(r, FUN=appmean, spat_alg = "bootspat_naive", spat_alg_args=list(random="species"),
                    aleats = aleats)
-  nms <- paste0(c("Observed", "Null_Mean", "Null_SD", "SES", "co_lower", "co_upper", "p_lower", "p_upper"), ".mean")
+  nms <- paste0(c("Observed", "Null_Mean", "Null_SD", "SES", "p_lower", "p_upper"), ".mean")
 
   expect_true(inherits(ses, "SpatRaster"), "TRUE")
   expect_true(terra::nlyr(ses) == length(nms))
   expect_named(ses, nms)
 
-  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), each=terra::nlyr(ses)/2)), nms))
+  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), c(4, 2))), nms))
 
-  expect_equal(unlist(ses[2]), setNames(c(0, 0.4, 0.11952286, -3.34664011, 5, 0, 1, 0), nms))
+  expect_equal(unlist(ses[2]), setNames(c(0, 0.4, 0.11952286, -3.34664011, 1, 0), nms))
 
   expect_equal(round(sd(terra::values(ses[[2]]), na.rm = TRUE), 3), as.double(0.081)) # test spat variation
 
@@ -31,7 +31,7 @@ test_that("SES works", {
   expect_true(terra::nlyr(ses) == length(nms))
   expect_named(ses, nms)
 
-  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), each=terra::nlyr(ses)/2)), nms))
+  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), c(4, 2))), nms))
 
   expect_equal(unlist(ses[2]), setNames(rep(0, length(nms)), nms))
 
@@ -46,7 +46,7 @@ test_that("SES works", {
   expect_true(terra::nlyr(ses) == length(nms))
   expect_named(ses, nms)
 
-  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), each=terra::nlyr(ses)/2)), nms))
+  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), c(4, 2))), nms))
 
   ## example with 'vec_alg'
   appsv <- function(x, lyrv, na.rm=T, ...){
@@ -63,8 +63,8 @@ test_that("SES works", {
                    aleats = aleats,
                    filename = paste0(tempfile(),"ses.tif"))
   # names(ses)
-  nms <- paste0(c("Observed", "Null_Mean", "Null_SD" ,"SES", "co_lower", "co_upper", "p_lower", "p_upper"), ".", n2)
-  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), each=terra::nlyr(ses)/2)), nms))
+  nms <- paste0(c("Observed", "Null_Mean", "Null_SD" ,"SES", "p_lower", "p_upper"), ".", n2)
+  expect_equal(unlist(ses[1]), setNames(as.double(rep(c(NA, 0), c(4, 2))), nms))
 
   expect_equal(unlist(ses[2]), setNames(rep(0, length(nms)), nms))